gufe.components.explicitmoleculecomponent

Classes

ExplicitMoleculeComponent(rdkit[, name])

Base class for explicit molecules.

class gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent(rdkit: rdkit.Chem.rdchem.Mol, name: str = '')

Base class for explicit molecules. Assumes that the molecule can be represented as an rdkit.Chem.Mol object.

Provides basic serialization and conversion to different representations. Specific file formats, such as SDF for small molecules or PDB for proteins, should be implemented in subclasses.

property name: str

property smiles: str

property total_charge

Net formal charge for the Component, if defined.

to_rdkit() → rdkit.Chem.rdchem.Mol

Return an RDKit copied representation of this molecule

classmethod from_rdkit(rdkit: rdkit.Chem.rdchem.Mol, name: str = '')

Create a Component, copying from an RDKit Mol

validate()

Validate this Component.

This method may be overridden by subclasses to implement component-specific consistency or sanity checks.

Implementations should raise an exception if validation fails. The base implementation performs no checks.